1) Only stayed in one guesthouse (in Kinlochbervie) and it was just me and one other couple, I just walked up and knocked on the door after deciding I couldn't be bothered with the tent that night. Couldn't stay at Inchnadamph as they had been booked out by a school group, so phone ahead for that one if it's on your route. I have only once found a bothy too full to stay in and that was much closer to civilisation than the North end of the Cape Wrath Trail
Worst case is you pitch up outside then sit indoors during the evening to socialise and get out of the midgies, then retire to your tent at night. Probably the best option full stop actually, no one else keeping you awake snoring!
2) I don't know the 'official' route but starting at Inverlael just looks like a lot of extra tarmac to Ullapool? Wouldn't be worth it I don't think.
3) The midgies will be out, how troublesome they are depends on how much you can tolerate them, the wind, your choice of repellant (if any) and how smokey your campfire is! A good reason to aim for bothies etc. so you can at least sit inside if they're bad, or camp high up or in exposed spots.
4) Harvey's are good maps in my experience, don't know if they cover that area though? OS would be ideal too.
5) I wasn't aware getting back out was a problem, the minibus was running when I was there however I was on my bike so just pedalled out. Think the ferry man just went back and forth depending on the queues but worth checking nearer the time. Also worth finding the freephone number for the firing range as you don't want to be crossing the Parph when they're bombing it!
Enjoy.